MCAT Biochemistry Review

Chapter 10: Carbohydrate Metabolism II: Aerobic Respiration

Conclusion

Both topics discussed in this chapter—the citric acid cycle and oxidative phosphorylation—take place in the mitochondria. In the mitochondrial matrix, the citric acid cycle completely oxidizes acetyl-CoA to carbon dioxide. While this happens, energy is conserved via reduction reactions, forming high-energy electron carriers such as FADH2 and NADH. ATP is also indirectly formed via GTP synthesis. These electron-rich carriers then transfer their electrons to the electron transport chain, which is located along the inner mitochondrial membrane. A series of oxidation–reduction reactions occur in specific complexes until oxygen, the final electron acceptor, gets reduced and forms H2O. This electrical pathway generates an electrochemical proton gradient that is harnessed by ATP synthase to generate ATP. The link between these two processes is highlighted by the fact that control of the citric acid cycle is NADH-dependent. When NADH accumulates, isocitrate dehydrogenase inhibition occurs, thus stopping both the citric acid cycle and electron transport chain.

It is worth noting that, while glycolysis is a major source of acetyl-CoA for the citric acid cycle, fatty acids also serve as an important source. In the next chapter, we turn our attention to the metabolism of two other types of biomolecules: lipids and amino acids.

Concept Summary

Acetyl-CoA

·        Acetyl-CoA contains a high-energy thioester bond that can be used to drive other reactions when hydrolysis occurs.

·        It can be formed from pyruvate via pyruvate dehydrogenase complex, a five-enzyme complex in the mitochondrial matrix that forms—and is also inhibited by—acetyl-CoA and NADH.

o   Pyruvate dehydrogenase (PDH) oxidizes pyruvate, creating CO2; it requires thiamine pyrophosphate (vitamin B1, TPP) and Mg2+.

o   Dihydropropyl transacetylase oxidizes the remaining two-carbon molecule using lipoic acid, and transfers the resulting acetyl group to CoA, forming acetyl-CoA.

o   Dihydrolipoyl dehydrogenase uses FAD to reoxidize lipoic acid, forming FADH2. This FADH2 can later transfer electrons to NAD+, forming NADH that can feed into the electron transport chain.

o   Pyruvate dehydrogenase kinase phosphorylates PDH when ATP or acetyl-CoA levels are high, turning it off.

o   Pyruvate dehydrogenase phosphatase dephosphorylates PDH when ADP levels are high, turning it on.

·        Acetyl-CoA can be formed from fatty acids, which enter the mitochondria using carriers.

o   The fatty acid couples with CoA in the cytosol to form fatty acyl-CoA, which moves to the intermembrane space.

o   The acyl (fatty acid) group is transferred to carnitine to form acyl-carnitine, which crosses the inner membrane.

o   The acyl group is transferred to a mitochondrial CoA to re-form fatty acyl-CoA, which can undergo β-oxidation to form acetyl-CoA.

·        Acetyl-CoA can be formed from the carbon skeletons of ketogenic amino acids, ketone bodies, and alcohol.

Reactions of the Citric Acid Cycle

·        The citric acid cycle takes place in mitochondrial matrix.

·        Its main purpose is to oxidize acetyl-CoA to CO2 and generate high-energy electron carriers (NADH and FADH2) and GTP.

·        Key enzymes and reactions:

o   Citrate synthase couples acetyl-CoA to oxaloacetate and then hydrolyzes the resulting product, forming citrate and CoA–SH. This enzyme is regulated by negative feedback from ATP, NADH, succinyl-CoA, and citrate.

o   Aconitase isomerizes citrate to isocitrate.

o   Isocitrate dehydrogenase oxidizes and decarboxylates isocitrate to form α-ketoglutarate. This enzyme generates the first CO2 and first NADH of the cycle. As the rate-limiting step of the citric acid cycle, it is heavily regulated: ATP and NADH are inhibitors; ADP and NAD+are activators.

o   α-Ketoglutarate dehydrogenase complex acts similarly to PDH complex, metabolizing α-ketoglutarate to form succinyl-CoA. This enzyme generates the second CO2 and second NADH of the cycle. It is inhibited by ATP, NADH, and succinyl-CoA; it is activated by ADP and Ca2+.

o   Succinyl-CoA synthetase hydrolyzes the thioester bond in succinyl-CoA to form succinate and CoA–SH. This enzyme generates the one GTP generated in the cycle.

o   Succinate dehydrogenase oxidizes succinate to form fumarate. This flavoprotein is anchored to the inner mitochondrial membrane because it requires FAD, which is reduced to form the one FADH2 generated in the cycle.

o   Fumarase hydrolyzes the alkene bond of fumarate, forming malate.

o   Malate dehydrogenase oxidizes malate to oxaloacetate. This enzyme generates the third and final NADH of the cycle.

The Electron Transport Chain

·        The electron transport chain takes place on the matrix-facing surface of the inner mitochondrial membrane.

·        NADH donates electrons to the chain, which are passed from one complex to the next. As the ETC progresses, reduction potentials increase until oxygen, which has the highest reduction potential, receives the electrons.

o   Complex I (NADH-CoQ oxidoreductase) uses an iron–sulfur cluster to transfer electrons from NADH to flavin mononucleotide (FMN), and then to coenzyme Q (CoQ), forming CoQH2. Four protons are translocated by Complex I.

o   Complex II (Succinate-CoQ oxidoreductase) uses an iron–sulfur cluster to transfer electrons from succinate to FAD, and then to CoQ, forming CoQH2. No proton pumping occurs at Complex II.

o   Complex III (CoQH2-cytochrome c oxidoreductase) uses an iron–sulfur cluster to transfer electrons from CoQH2 to heme, forming cytochrome c as part of the Q cycle. Four protons are translocated by Complex III.

o   Complex IV (cytochrome c oxidase) uses cytochromes and Cu2+ to transfer electrons in the form of hydride ions (H) from cytochrome c to oxygen, forming water. Two protons are translocated by Complex IV.

·        NADH cannot cross the inner mitochondrial membrane. Therefore, one of two available shuttle mechanisms to transfer electrons in the mitochondrial matrix must be used.

o   In the glycerol 3-phosphate shuttle, electrons are transferred from NADH to dihydroxyacetone phosphate (DHAP), forming glycerol 3-phosphate. These electrons can then be transferred to mitochondrial FAD, forming FADH2.

o   In the malate–aspartate shuttle, electrons are transferred from NADH to oxaloacetate, forming malate. Malate can then cross the inner mitochondrial membrane and transfer the electrons to mitochondrial NAD+, forming NADH.

Oxidative Phosphorylation

·        The proton-motive force is the electrochemical gradient generated by the electron transport chain across the inner mitochondrial membrane. The intermembrane space has a higher concentration of protons than the matrix; this gradient stores energy, which can be used to form ATP viachemiosmotic coupling.

·        ATP synthase is the enzyme responsible for generating ATP from ADP and an inorganic phosphate (Pi).

o   The F0 portion is an ion channel, allowing protons to flow down the gradient from the intermembrane space to the matrix.

o   The F1 portion uses the energy released by the gradient to phosphorylate ADP into ATP.

·        The following is a summary of the energy yield of the various carbohydrate metabolism processes:

o   Glycolysis generates 2 NADH and 2 ATP.

o   Pyruvate dehydrogenase generates 1 NADH per molecule of pyruvate. Because each glucose forms two molecules of pyruvate, this complex produces a net of 2 NADH.

o   The citric acid cycle generates 3 NADH, 1 FADH2, and 1 GTP (6 NADH, 2 FADH2, and 2 GTP per molecule of glucose).

o   Each NADH yields 2.5 ATP; 10 NADH form 25 ATP.

o   Each FADH2 yields 1.5 ATP; 2 FADH2 form 3 ATP.

o   GTP are converted to ATP.

o   2 ATP from glycolysis + 2 ATP (GTP) from the citric acid cycle + 25 ATP from NADH + 3 ATP from FADH2 = 32 ATP per molecule of glucose (optimal). Inefficiencies of the system and variability between cells make 30-32 ATP/glucose the commonly accepted range for energy yield.

Answers to Concept Checks

·        10.1

1.    Pyruvate + CoA–SH + NAD+ → acetyl-CoA + CO2 + NADH + H+

2.     

Molecule

Mechanism of Conversion to Acetyl-CoA

Fatty acids

Shuttle acyl group from cytosolic CoA-SH to mitochondrial CoA-SH via carnitine; then undergo β-oxidation

Ketogenic amino acids

Transaminate to lose nitrogen; convert carbon skeleton into ketone body, which can be converted into acetyl-CoA

Ketones

Reverse of ketone body formation; actual enzyme names are out of scope for the MCAT

Alcohol

Alcohol dehydrogenase and acetaldehyde dehydrogenase convert alcohol into acetyl-CoA

·        10.2

1.    Complete oxidation of acetyl-CoA to CO2 so that reduction reactions can be coupled with CO2 formation, thus forming energy carriers such as NADH and FADH2 for the electron transport chain.

2.    Isocitrate dehydrogenase.

3.     

Checkpoints

Inhibitors

Activators

Citrate synthase

ATP, NADH, succinyl-CoA, citrate

None

Isocitrate dehydrogenase

ATP, NADH

ADP, NAD+

α-Ketoglutarate complex

ATP, NADH, succinyl-CoA

ADP, Ca2+

·        10.3

1.     

·        Pumping a proton into the intermembrane space: I, III, and IV

·        Acquiring electrons from NADH: I

·        Acquiring electrons from FADH2: II

·        Having the highest reduction potential: IV (reduction potentials increase along the ETC)

2.    The electron transport chain generates the proton-motive force, an electrochemical gradient across the inner mitochondrial membrane, which provides the energy for ATP synthase to function.

3.    The malate–aspartate shuttle. Because this mechanism is the more efficient one, it makes sense for a highly aerobic organ such as the heart to utilize it in order to maximize its ATP yield.

·        10.4

1.    The ETC is made up of the physical set of intermembrane proteins located on the inner mitochondrial matrix, and they undergo redox reactions as they transfer electrons to oxygen, the final electron acceptor. As electrons are transferred, a proton-motive force is generated in the intermembrane space. Oxidative phosphorylation is the process by which ATP is generated via harnessing the proton gradient, and it utilizes ATP synthase to do so.

2.    By splitting up electron transfer into several complexes, enough energy is released to facilitate the creation of a proton gradient at many locations, rather than just one. The greater the proton gradient is, the greater the ATP generation will be. Direct reduction of oxygen by NADH would release a significant amount of energy to the environment, resulting in inefficient electron transport.

Shared Concepts

·        Biochemistry Chapter 2

o   Enzymes

·        Biochemistry Chapter 4

o   Carbohydrate Structure and Function

·        Biochemistry Chapter 9

o   Carbohydrate Metabolism I

·        Biochemistry Chapter 11

o   Lipid and Amino Acid Metabolism

·        Biochemistry Chapter 12

o   Bioenergetics and Regulation of Metabolism

·        General Chemistry Chapter 12

o   Electrochemistry